BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234088.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 936,572 number of mapped reads = 642,258 (68.58%) number of supplementary alignments = 3,189 (0.34%) number of secondary alignments = 0 number of mapped bases = 40,644,607 bp number of sequenced bases = 40,624,138 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,936 duplication rate = 1.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8387 >>>>>>> ACTG content number of A's = 11,459,008 bp (28.21%) number of C's = 6,691,255 bp (16.47%) number of T's = 13,091,966 bp (32.23%) number of G's = 9,374,315 bp (23.08%) number of N's = 7,594 bp (0.02%) GC percentage = 39.55% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 383,707 number of insertions = 3,150 mapped reads with insertion percentage = 0.49% number of deletions = 11,951 mapped reads with deletion percentage = 1.84% homopolymer indels = 45.71% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.1541X There is a 1.23% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4661447 0.018701847085869448 0.24005073558840312 chr2 243199373 2161162 0.008886379818092704 0.12935924264835166 chr3 198022430 4269926 0.021562840128767233 0.15439530037198282 chr4 191154276 1722859 0.009012924199508882 0.10099694954781292 chr5 180915260 2327373 0.012864437195624074 0.1191743403188245 chr6 171115067 2481335 0.01450097319600734 0.1359265620990463 chr7 159138663 2473821 0.015545065877548564 0.1727439080270339 chr8 146364022 2221301 0.01517655069631798 0.3011922439995373 chr9 141213431 1283577 0.009089624059909712 0.11612661784874806 chr10 135534747 1857342 0.013703806891674797 0.13780183520304684 chr11 135006516 1662950 0.01231755362089338 0.13081742008792988 chr12 133851895 1489853 0.011130608199458065 0.1106525327336448 chr13 115169878 1710712 0.014853814467008465 0.1278248698549562 chr14 107349540 2158762 0.020109653008294214 0.15140600507755603 chr15 102531392 852542 0.008314936366025344 0.09536961372210806 chr16 90354753 801787 0.008873766718171429 0.10356600952254898 chr17 81195210 987101 0.01215713340725395 0.1194492578571003 chr18 78077248 992691 0.012714216054336341 0.19806719557282895 chr19 59128983 954651 0.01614522948923373 0.15690214391886576 chr20 63025520 947669 0.015036274194961025 0.12946677827075345 chr21 48129895 947478 0.019685852213058016 0.14897378054446445 chr22 51304566 346288 0.006749652652748296 0.08605404638545194 chrMT 16571 37690 2.2744553738458753 2.1746063686299926 chrX 155270560 1205495 0.0077638349472044154 0.09686956683756481 chrY 59373566 88795 0.0014955308562736487 0.045973076134353655